Genome-wide identification of Aux/IAA gene family in white clover (Trifolium repens L.) and functional verification of TrIAA18 under different abiotic stress

BACKGROUND

White clover (Trifolium repens L.) is an excellent leguminous cool-season forage with a high protein content and strong nitrogen-fixing ability. Despite these advantages, its growth and development are markedly sensitive to environmental factors. Indole-3-acetic acid (IAA) is the major growth hormone in plants, regulating plant growth, development, and response to adversity. Nevertheless, the specific regulatory functions of Aux/IAA genes in response to abiotic stresses in white clover remain largely unexplored.

RESULTS

In this study, we identified 47 Aux/IAA genes in the white clover genome, which were categorized into five groups based on phylogenetic analysis. The TrIAAs promoter region co-existed with different cis-regulatory elements involved in developmental and hormonal regulation, and stress responses, which may be closely related to their diverse regulatory roles. Collinearity analysis showed that the amplification of the TrIAA gene family was mainly carried out by segmental duplication. White clover Aux/IAA genes showed different expression patterns in different tissues and under different stress treatments. In addition, we performed a yeast two-hybrid analysis to investigate the interaction between white clover Aux/IAA and ARF proteins. Heterologous expression indicated that TrIAA18 could enhance stress tolerance in both yeast and transgenic Arabidopsis thaliana.

CONCLUSION

These findings provide new scientific insights into the molecular mechanisms of growth hormone signaling in white clover and its functional characteristics in response to environmental stress.

Drought priming-induced stress memory improves subsequent drought or heat tolerance via activation of γ-aminobutyric acid-regulated pathways in creeping bentgrass

Recurrent drought can induce stress memory in plants to induce tolerance to subsequent stress, such as high temperature or drought. Drought priming (DP) is an effective approach to improve tolerance to various stresses; however, the potential mechanism of DP-induced stress memory has not been fully resoved. We examined DP-regulated subsequent drought tolerance or thermotolerance associated with changes in physiological responses, GABA and NO metabolism, heat shock factor (HSF) and dehydrin (DHN) pathways in perennial creeping bentgrass. Plants can recover after two cycle of DP, and DP-treated plants had significantly higher tolerance to subsequent drought or heat stress, with higher leaf RWC, Chl content, photochemical efficiency, and cell membrane stability. DP significantly alleviated oxidative damage through enhancing total antioxidant capacity in response to subsequent drought or heat stress. Endogenous GABA was significantly increased by DP through activating glutamic acid decarboxylase activity and inhibiting GABA transaminase activity. DP also enhanced accumulation of NO, depending on NOS activity, under subsequent drought or heat stress. Transcript levels of multiple transcription factors, heat shock proteins, and DHNs in the HSF and DHN pathways were up-regulated by DP under drought or heat stress, but there were differences between DP-regulated heat tolerance and drought tolerance in these pathways. The findings indicate that under recurrent moderate drought, DP improves subsequent tolerance to drought or heat stress in relation to GABA-regulated pathways, providing new insight into understanding of the role of stress memory in plant adaptation to complex environmental stresses.

Spermidine or spermine pretreatment regulates organic metabolites and ions homeostasis in favor of white clover seed germination against salt toxicity

White clover is widely cultivated as a leguminous forage or ground cover plant worldwide. However, soil salinization decreases its yield and quality. Aims of the present experiment were to elucidate the impact of seed pretreatment with spermidine (Spd) or spermine (Spm) on amylolysis, Na+/K+ accumulation, and metabolic homeostasis during germination. Seed was soaked in distilled water (control), Spd or Spm solution and then germinated under optimal or salt stress conditions for 7 days. Results showed that germination vigor, germination percentage, or seed vigour index of seeds pretreatment with Spd increased by 7%, 11%, or 70% when compared with water-pretreated seeds under salt stress, respectively. Germination percentage or seed vigour index of seeds pretreatment with Spm increased by 17% or 78% than water-pretreated seeds under saline condition, respectively. In response to salt stress, accelerated amylolysis via activation of β-amylase activity was induced by Spd or Spm pretreatment. Spd or Spm pretreatment also significantly enhanced accumulation of diverse amino acids, organic acids, sugars, and other metabolites (putrescine, myo-inositol, sorbitol, daidzein etc.) associated with enhanced osmotic adjustment, antioxidant capacity, and energy supply during germination under salt stress. In addition, Spd or Spm pretreatment not only significantly reduced salt-induced K+ loss and overaccumulation of Na+, but also improved the ratio of K+ to Na+, contributing to Na+ and K+ balance in seedlings. In response to salt stress, seeds pretreatment with Spd or Spm up-regulated transcription level of NHX2 related to enhancement in compartmentation of Na+ from cytoplasm to vacuole, thus reducing Na+ toxicity in cytoplasm. Spm priming also uniquely up-regulated transcription levels of SKOR, HKT1, and HAL2 associated with K+ and Na + homeostasis and decline in cytotoxicity under salt stress.

Optimization of Protocols for the Induction of Callus and Plant Regeneration in White Clover (Trifolium repens L.)

White clover is a widely grown temperate legume forage with high nutritional value. Research on the functional genomics of white clover requires a stable and efficient transformation system. In this study, we successfully induced calluses from the cotyledons and leaves of 10 different white clover varieties. The results showed that the callus formation rate in the cotyledons did not vary significantly among the varieties, but the highest callus formation rate was observed in 'Koala' leaves. Subsequently, different concentrations of antioxidants and hormones were tested on the browning rate and differentiation ability of the calluses, respectively. The results showed that the browning rate was the lowest on MS supplemented with 20 mg L^-1 AgNO₃ and 25 mg L^-1 VC, respectively, and the differentiation rate was highest on MS supplemented with 1 mg L^-1 6-BA, 1 mg L^-1 KT and 0.5 mg L^-1 NAA. In addition, the transformation system for Agrobacterium tumefaciens-mediated transformation of 4-day-old leaves was optimized to some extent and obtained a positive callus rate of 8.9% using green fluorescent protein (GFP) as a marker gene. According to our data, by following this optimized protocol, the transformation efficiency could reach 2.38%. The results of this study will provide the foundation for regenerating multiple transgenic white clover from a single genetic background.

A Trifolium repens flavodoxin-like quinone reductase 1 (TrFQR1) improves plant adaptability to high temperature associated with oxidative homeostasis and lipids remodeling

Maintenance of stable mitochondrial respiratory chains could enhance adaptability to high temperature, but the potential mechanism was not elucidated clearly in plants. In this study, we identified and isolated a TrFQR1 gene encoding the flavodoxin-like quinone reductase 1 (TrFQR1) located in mitochondria of leguminous white clover (Trifolium repens). Phylogenetic analysis indicated that amino acid sequences of FQR1 in various plant species showed a high degree of similarities. Ectopic expression of TrFQR1 protected yeast (Saccharomyces cerevisiae) from heat damage and toxic levels of benzoquinone, phenanthraquinone and hydroquinone. Transgenic Arabidopsis thaliana and white clover overexpressing TrFQR1 exhibited significantly lower oxidative damage and better photosynthetic capacity and growth than wild-type in response to high-temperature stress, whereas AtFQR1-RNAi A. thaliana showed more severe oxidative damage and growth retardation under heat stress. TrFQR1-transgenic white clover also maintained better respiratory electron transport chain than wild-type plants, as manifested by significantly higher mitochondrial complex II and III activities, alternative oxidase activity, NAD(P)H content, and coenzyme Q10 content in response to heat stress. In addition, overexpression of TrFQR1 enhanced the accumulation of lipids including phosphatidylglycerol, monogalactosyl diacylglycerol, sulfoquinovosyl diacylglycerol and cardiolipin as important compositions of bilayers involved in dynamic membrane assembly in mitochondria or chloroplasts positively associated with heat tolerance. TrFQR1-transgenic white clover also exhibited higher lipids saturation level and phosphatidylcholine:phosphatidylethanolamine ratio, which could be beneficial to membrane stability and integrity during a prolonged period of heat stress. The current study proves that TrFQR1 is essential for heat tolerance associated with mitochondrial respiratory chain, cellular reactive oxygen species homeostasis, and lipids remodeling in plants. TrFQR1 could be selected as a key candidate marker gene to screen heat-tolerant genotypes or develop heat-tolerant crops via molecular-based breeding.

Primary plant nutrients modulate the reactive oxygen species metabolism and mitigate the impact of cold stress in overseeded perennial ryegrass

Overseeded perennial ryegrass (Lolium perenne L.) turf on dormant bermudagrass (Cynodon dactylon Pers. L) in transitional climatic zones (TCZ) experience a severe reduction in its growth due to cold stress. Primary plant nutrients play an important role in the cold stress tolerance of plants. To better understand the cold stress tolerance of overseeded perennial ryegrass under TCZ, a three-factor and five-level central composite rotatable design (CCRD) with a regression model was used to study the interactive effects of nitrogen (N), phosphorus (P), and potassium (K) fertilization on lipid peroxidation, electrolyte leakage, reactive oxygen species (ROS) production, and their detoxification by the photosynthetic pigments, enzymatic and non-enzymatic antioxidants. The study demonstrated substantial effects of N, P, and K fertilization on ROS production and their detoxification through enzymatic and non-enzymatic pathways in overseeded perennial ryegrass under cold stress. Our results demonstrated that the cold stress significantly enhanced malondialdehyde, electrolyte leakage, and hydrogen peroxide contents, while simultaneously decreasing ROS-scavenging enzymes, antioxidants, and photosynthetic pigments in overseeded perennial ryegrass. However, N, P, and K application mitigated cold stress-provoked adversities by enhancing soluble protein, superoxide dismutase, peroxide dismutase, catalase, and proline contents as compared to the control conditions. Moreover, N, P, and, K application enhanced chlorophyll a, chlorophyll b, total chlorophyll, and carotenoids in overseeded perennial ryegrass under cold stress as compared to the control treatments. Collectively, this 2-years study indicated that N, P, and K fertilization mitigated cold stress by activating enzymatic and non-enzymatic antioxidants defense systems, thereby concluding that efficient nutrient management is the key to enhanced cold stress tolerance of overseeded perennial ryegrass in a transitional climate. These findings revealed that turfgrass management will not only rely on breeding new varieties but also on the development of nutrient management strategies for coping cold stress.

Effect of different planting pattern arrangements on soil organic matter and soil nitrogen content under a maize/soybean strip relay intercropping system

Assessing the spatial distribution of organic matter and total nitrogen in soil is essential for management and optimum utilization of fertilizers. Therefore, the present field experiment was conducted to evaluate the impact of different planting pattern arrangements on the spatial distribution of soil total nitrogen and organic matter content under a maize/soybean strip relay intercropping system. The planting was arranged in a manner such that soil sampling could be done from continuous maize/soybean relay strip intercropping (MS1), maize/soybean relay strip intercropping in rotation (MS2), traditional maize/soybean intercropping (MS3), sole maize (M), sole soybean (S), and fallow land (FL) from 2018 to 2020. The results showed significant variations for soil organic matter and total nitrogen content under different planting pattern arrangements of maize and soybean in the strip relay intercropping system. Across all systems, the highest soil organic matter (29.19 g/kg) and total nitrogen (10.19 g/kg) were recorded in MS2. In contrast, the lowest soil organic matter (1.69 g/kg) and total nitrogen (0.64 g/kg) were observed in FL. Soil organic matter and total nitrogen in MS2 increased by 186.45% and 164.06%, respectively, when compared with FL. Soil organic matter and total nitrogen in MS2 increased by 186.45% and 164.06%, respectively, when compared with FL. Furthermore, under MS2, the spatial distribution of soil organic matter was higher in both maize and soybean crop rows as compared with other cropping patterns, whereas the soil total nitrogen was higher under soybean rows as compared with maize in all other treatment. However, correlation analysis of the treatments showed variations in organic matter content. It can be concluded that different planting patterns can have varying effects on soil organic matter and total nitrogen distribution under the strip relay intercropping system. Moreover, it is recommended from this study that MS2 is a better planting pattern for the strip relay intercropping system, which can increase the spatial distribution of soil organic matter and total nitrogen, thereby improving soil fertility, C:N ratio, and crop production. This study will serve as a foundation towards the scientific usage of chemical fertilizers in agricultural sector.

Genetic Testing to Inform Epilepsy Treatment Management From an International Study of Clinical Practice

Importance

It is currently unknown how often and in which ways a genetic diagnosis given to a patient with epilepsy is associated with clinical management and outcomes.

Objective

To evaluate how genetic diagnoses in patients with epilepsy are associated with clinical management and outcomes.

Design, Setting, and Participants

This was a retrospective cross-sectional study of patients referred for multigene panel testing between March 18, 2016, and August 3, 2020, with outcomes reported between May and November 2020. The study setting included a commercial genetic testing laboratory and multicenter clinical practices. Patients with epilepsy, regardless of sociodemographic features, who received a pathogenic/likely pathogenic (P/LP) variant were included in the study. Case report forms were completed by all health care professionals.

Exposures

Genetic test results.

Main Outcomes and Measures

Clinical management changes after a genetic diagnosis (ie, 1 P/LP variant in autosomal dominant and X-linked diseases; 2 P/LP variants in autosomal recessive diseases) and subsequent patient outcomes as reported by health care professionals on case report forms.

Results

Among 418 patients, median (IQR) age at the time of testing was 4 (1-10) years, with an age range of 0 to 52 years, and 53.8% (n = 225) were female individuals. The mean (SD) time from a genetic test order to case report form completion was 595 (368) days (range, 27-1673 days). A genetic diagnosis was associated with changes in clinical management for 208 patients (49.8%) and usually (81.7% of the time) within 3 months of receiving the result. The most common clinical management changes were the addition of a new medication (78 [21.7%]), the initiation of medication (51 [14.2%]), the referral of a patient to a specialist (48 [13.4%]), vigilance for subclinical or extraneurological disease features (46 [12.8%]), and the cessation of a medication (42 [11.7%]). Among 167 patients with follow-up clinical information available (mean [SD] time, 584 [365] days), 125 (74.9%) reported positive outcomes, 108 (64.7%) reported reduction or elimination of seizures, 37 (22.2%) had decreases in the severity of other clinical signs, and 11 (6.6%) had reduced medication adverse effects. A few patients reported worsening of outcomes, including a decline in their condition (20 [12.0%]), increased seizure frequency (6 [3.6%]), and adverse medication effects (3 [1.8%]). No clinical management changes were reported for 178 patients (42.6%).

Conclusions and Relevance

Results of this cross-sectional study suggest that genetic testing of individuals with epilepsy may be materially associated with clinical decision-making and improved patient outcomes.

A Heat Shock Transcription Factor TrHSFB2a of White Clover Negatively Regulates Drought, Heat and Salt Stress Tolerance in Transgenic Arabidopsis

Heat shock transcription factors (HSF) are divided into classes A, B and C. Class A transcription factors are generally recognized as transcriptional activators, while functional characterization of class B and C heat shock transcription factors have not been fully developed in most plant species. We isolated and characterized a novel HSF transcription factor gene, TrHSFB2a (a class B HSF) gene, from the drought stress-sensitive forage crop species, white clover (Trifolium repens). TrHSFB2a was highly homologous to MtHSFB2b, CarHSFB2a, AtHSFB2b and AtHSFB2a. The expression of TrHSFB2a was strongly induced by drought (PEG6000 15% w/v), high temperature (35 °C) and salt stresses (200 mM L-1 NaCl) in white clover, while subcellular localization analysis showed that it is a nuclear protein. Overexpression of the white clover gene TrHSFB2a in Arabidopsis significantly reduced fresh and dry weight, relative water contents (RWC), maximum photosynthesis efficiency (Fv/Fm) and performance index on the absorption basis (PIABS), while it promoted leaf senescence, relative electrical conductivity (REC) and the contents of malondialdehyde (MDA) compared to a wild type under drought, heat and salt stress conditions of Arabidopsis plants. The silencing of its native homolog (AtHSFB2a) by RNA interference in Arabidopsis thaliana showed opposite trends by significantly increasing fresh and dry weights, RWC, maximum photosynthesis efficiency (Fv/Fm) and performance index on the absorption basis (PIABS) and reducing REC and MDA contents under drought, heat and salt stress conditions compared to wild type Arabidopsis plants. These phenotypic and physiological indicators suggested that the TrHSFB2a of white clover functions as a negative regulator of heat, salt and drought tolerance. The bioinformatics analysis showed that TrHSFB2a contained the core B3 repression domain (BRD) that has been reported as a repressor activator domain in other plant species that might repress the activation of the heat shock-inducible genes required in the stress tolerance process in plants. The present study explores one of the potential causes of drought and heat sensitivity in white clover that can be overcome to some extent by silencing the TrHSFB2a gene in white clover.

Enhanced Adaptability to Limited Water Supply Regulated by Diethyl Aminoethyl Hexanoate (DA-6) Associated With Lipidomic Reprogramming in Two White Clover Genotypes

Membrane lipid reprogramming is one of the most important adaptive strategies in plant species under unfavorable environmental circumstances. Therefore, the present experiment was conducted to elucidate the effect of diethyl aminoethyl hexanoate (DA-6), a novel synthetic plant growth regulator, on oxidative damage, photosynthetic performance, changes in lipidomic profile, and unsaturation index of lipids in two white clover (Trifolium repens) cultivars (drought-sensitive "Ladino" and drought-resistant "Riverdel") under PEG-6000-induced water-deficit stress. Results revealed that water-deficit stress significantly enhanced oxidative damage and decreased photosynthetic functions in both cultivars. However, the damage was less in Riverdel. In addition, water-deficit stress significantly decreased the relative content of monogalactocyl-diacylglycerols (MGDG), sulfoquinovosyl-diacylglycerols (SQDG), phosphatidic acisd (PA), phosphatidyl-ethanolamines (PE), phosphatidyl-glycerols (PG), phosphatidyl-serines (PS), ceramides (Cer), hexosylmonoceramides (Hex1Cer), sphingomyelins (SM), and sphingosines (Sph) in both cultivars, but a more pronounced decline was observed in Ladino. Exogenous application of DA-6 significantly increased the relative content of digalactocyl-diacylglycerols (DGDG), monogalactocyl-diacylglycerolsabstra (MGDG), sulfoquinovosyl-diacylglycerols (SQDG), phosphatidic acids (PA), phosphatidyl-ethanolamines (PE), phosphatidyl-glycerols (PG), phosphatidyl-inositols (PI), phosphatidyl-serines (PS), ceramides (Cer), hexosylmonoceramides (Hex1Cer), neutral glycosphingolipids (CerG2GNAc1), and sphingosines (Sph) in the two cultivars under water-deficit stress. DA-6-treated Riverdel exhibited a significantly higher DGDG:MGDG ratio and relative content of sphingomyelins (SM) than untreated plants in response to water deficiency. Furthermore, the DA-6-pretreated plants increased the unsaturation index of phosphatidic acids (PA) and phosphatidylinositols (PI) in Ladino, ceramides (Cer) and hexosylmonoceramides (Hex1Cer) in Riverdel, and sulfoquinovosyl-diacylglycerols (SQDG) in both cultivars under water stress. These results suggested that DA-6 regulated drought resistance in white clover could be associated with increased lipid content and reprogramming, higher DGDG:MGDG ratio, and improved unsaturation index of lipids, contributing to enhanced membrane stability, integrity, fluidity, and downstream signaling transduction.

Metabolites Reprogramming and Na+/K+ Transportation Associated With Putrescine-Regulated White Clover Seed Germination and Seedling Tolerance to Salt Toxicity

Soil salinization is a serious challenge to many countries worldwide. Putrescine (Put) is related to the improvement of seed germination under salt stress, but molecular and metabolic mechanisms are still not fully understood. The objectives of this study were to determine the effect of seed soaking with Put on germination characteristics under salt stress induced by 100 mm sodium chloride (NaCl) and to further analyze subsequent stress tolerance associated with amylolysis, oxidative damage, sodium (Na+)/ potassium (K+) accumulation and transportation, and metabolic homeostasis in white clover (Trifolium repens cv. Haifa) seedlings. The results showed that seed soaking with Put significantly alleviated salt-induced decreases in the endogenous Put content, germination rate, germination vigor, germination index, Rl/SL, and fresh/dry weight of seedlings. Put application also significantly promoted starch metabolism through activating α-amylase and β-amylase activities under salt stress. The metabolomic analysis showed that seed soaking with Put significantly increased the accumulation of polyamines (Put and spermidine), amino acids (γ-aminobutyric acid, glutamate, alanine, proline, citrulline, etc.), organic acids (ketopentanic acid, malonic acid, malic acid, ketopentanic acid, cis-sinapinic acid, etc.), lipids and fatty acids (glycerol, stearic acid, linoleic acid, palmitic acid, etc.), sugars (levoglucosan, fucose, and anhydro-D-galactose), alcohols (myo-inositol, allo-inositol, hexadecanol, and threitol), and other metabolites (thymine, xanthine, adenine, guanine, and glycerol 1-phosphate, etc.) associated with enhanced tricarboxylic acid (TCA) cycle and γ-aminobutyric acid (GABA) shunt contributing to better osmotic adjustment, cell membrane stability, energy supply, and metabolic homeostasis when seeds germinated under salt stress. In addition, Put significantly up-regulated the AsSOS1, NHX6, SKOR, HKT1, and HKT8 expression levels which played critical roles in Na+ rejection and K+ retention resulting in higher K+/Na+ ratio during seed germination under salt stress. The Put-induced up-regulation of HAL2 transcription level could reduce the toxicity of 3'-phosphoadenosine-5'-phosphosulfate (PAPS) in cells. Current findings will provide an integrative understanding of Put-induced salt tolerance associated with amylolysis, metabolic regulation, and ionic homeostasis during seed germination.

γ-Aminobutyric Acid (GABA) Priming Improves Seed Germination and Seedling Stress Tolerance Associated With Enhanced Antioxidant Metabolism, DREB Expression, and Dehydrin Accumulation in White Clover Under Water Stress

As an important plant growth regulator, the role of γ-aminobutyric acid (GABA) in regulating seeds germination was less well elucidated under water stress. The present study was conducted to investigate the impact of GABA pretreatment on seeds germination of white clover (Trifolium repens) under water deficient condition. Results demonstrated that seeds pretreated with 2μmol/l GABA significantly alleviated decreases in endogenous GABA content, germination percentage, germination potential, germination index, root length, and fresh weight along with marked reduction in mean germination time after 7days of germination under drought stress. In addition, seeds priming with GABA significantly increased the accumulation of soluble sugars, non-enzymatic antioxidants [reduced ascorbate, dehydroascorbic acid, oxidized glutathione (GSSG), and reduced glutathione (GSH)], and enzymes [superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), ascorbate peroxidase (APX), dehydroascorbate reductase (DHAR), glutathioe reductase, and monodehydroasorbate reductase (MDHR)] activities involved in antioxidant metabolism, which could be associated with significant reduction in osmotic potential and the accumulation of superoxide anion, hydrogen peroxide, electrical leakage, and malondialdehyde in seeds under drought stress. The GABA-pretreated seeds exhibited significantly higher abundance of dehydrin (DHN, 56 KDa) and expression levels of DHNs encoding genes (SK2, Y2K, Y2SK, and Dehydrin b) and transcription factors (DREB2, DREB3, DREB4, and DREB5) than the untreated seeds during germination under water-limited condition. These results indicated that the GABA regulated improvement in seeds germination associated with enhancement in osmotic adjustment, antioxidant metabolism, and DREB-related DHNs expression. Current study will provide a better insight about the GABA-regulated defense mechanism during seeds germination under water-limited condition.

Effects of silicon on heavy metal uptake at the soil-plant interphase: A review

Silicon (Si) is the second richest element in the soil and surface of earth crust with a variety of positive roles in soils and plants. Different soil factors influence the Si bioavailability in soil-plant system. The Si involves in the mitigation of various biotic (insect pests and pathogenic diseases) and abiotic stresses (salt, drought, heat, and heavy metals etc.) in plants by improving plant tolerance mechanism at various levels. However, Si-mediated restrictions in heavy metals uptake and translocation from soil to plants and within plants require deep understandings. Recently, Si-based improvements in plant defense system, cell damage repair, cell homeostasis, and regulation of metabolism under heavy metal stress are getting more attention. However, limited knowledge is available on the molecular mechanisms by which Si can reduce the toxicity of heavy metals, their uptake and transfer from soil to plant roots. Thus, this review is focused the following facets in greater detail to provide better understandings about the role of Si at molecular level; (i) how Si improves tolerance in plants to variable environmental conditions, (ii) how biological factors affect Si pools in the soil (iii) how soil properties impact the release and capability of Si to decrease the bioavailability of heavy metals in soil and their accumulation in plant roots; (iv) how Si influences the plant root system with respect to heavy metals uptake or sequestration, root Fe/Mn plaque, root cell wall and compartment; (v) how Si makes complexes with heavy metals and restricts their translocation/transfer in root cell and influences the plant hormonal regulation; (vi) the competition of uptake between Si and heavy metals such as arsenic, aluminum, and cadmium due to similar membrane transporters, and (vii) how Si-mediated regulation of gene expression involves in the uptake, transportation and accumulation of heavy metals by plants and their possible detoxification mechanisms. Furthermore, future research work with respect to mitigation of heavy metal toxicity in plants is also discussed.

Chitosan (CTS) Alleviates Heat-Induced Leaf Senescence in Creeping Bentgrass by Regulating Chlorophyll Metabolism, Antioxidant Defense, and the Heat Shock Pathway

Chitosan (CTS) is a deacetylated derivative of chitin that is involved in adaptive response to abiotic stresses. However, the regulatory role of CTS in heat tolerance is still not fully understood in plants, especially in grass species. The aim of this study was to investigate whether the CTS could reduce heat-induced senescence and damage to creeping bentgrass associated with alterations in antioxidant defense, chlorophyll (Chl) metabolism, and the heat shock pathway. Plants were pretreated exogenously with or without CTS (0.1 g L-1) before being exposed to normal (23/18 °C) or high-temperature (38/33 °C) conditions for 15 days. Heat stress induced detrimental effects, including declines in leaf relative water content and photochemical efficiency, but significantly increased reactive oxygen species (ROS) accumulation, membrane lipid peroxidation, and Chl loss in leaves. The exogenous application of CTS significantly alleviated heat-induced damage in creeping bentgrass leaves by ameliorating water balance, ROS scavenging, the maintenance of Chl metabolism, and photosynthesis. Compared to untreated plants under heat stress, CTS-treated creeping bentgrass exhibited a significantly higher transcription level of genes involved in Chl biosynthesis (AsPBGD and AsCHLH), as well as a lower expression level of Chl degradation-related gene (AsPPH) and senescence-associated genes (AsSAG12, AsSAG39, Asl20, and Ash36), thus reducing leaf senescence and enhancing photosynthetic performance under heat stress. In addition, the foliar application of CTS significantly improved antioxidant enzyme activities (SOD, CAT, POD, and APX), thereby effectively reducing heat-induced oxidative damage. Furthermore, heat tolerance regulated by the CTS in creeping bentgrass was also associated with the heat shock pathway, since AsHSFA-6a and AsHSP82 were significantly up-regulated by the CTS during heat stress. The potential mechanisms of CTS-regulated thermotolerance associated with other metabolic pathways still need to be further studied in grass species.

A 24-generation-old founder mutation impairs splicing of RBBP8 in Pakistani families affected with Jawad syndrome

Jawad syndrome is a multiple congenital anomaly and intellectual disability syndrome with mutation in RBBP8 reported only in two families. Here, we report on two new families from Pakistan and identified a previously reported variant in RBBP8, NM_002894.3:c.1808-1809delTA. We could show that this mutation impairs splicing resulting in two different abnormal transcripts. Finally, we could verify a shared haplotype among all four families and estimate the founder event to have occurred some 24 generations ago.

Diethyl Aminoethyl Hexanoate Priming Ameliorates Seed Germination via Involvement in Hormonal Changes, Osmotic Adjustment, and Dehydrins Accumulation in White Clover Under Drought Stress

Drought is a serious outcome of climate change reducing the productivity of forage species under arid and semi-arid conditions worldwide. Diethyl aminoethyl hexanoate (DA-6), a novel plant growth regulator, has proven to be involved in the amelioration of critical physiological functions in many agricultural crops under various abiotic stresses, but the role of the DA-6 in improving seed germination has never been investigated under drought stress. The present study was carried out to elucidate the impact of the DA-6 priming on seeds germination of white clover under drought stress. Results showed that seed priming with the DA-6 significantly mitigated the drought-induced reduction in germination percentage, germination vigor, germination index, seed vigor index, root length, shoot length, and fresh weight after 7 days of seed germination. The DA-6 significantly increased the endogenous indole-3-acetic acid, gibberellin, and cytokinin content with marked reduction in abscisic acid content in seedlings under drought stress. In addition, the DA-6 significantly accelerated starch catabolism by enhancing the activities of hydrolases contributing toward enhanced soluble sugars, proline content and ameliorated the antioxidant defense system to enhance the ability of reactive oxygen species scavenging under drought stress. Furthermore, exogenous DA-6 application significantly increased dehydrins accumulation and upregulated transcript levels of genes encoding dehydrins (SK2, Y2SK, or DHNb) during seeds germination under water deficient condition. These findings suggested that the DA-6 mediated seeds germination and drought tolerance associated with changes in endogenous phytohormones resulting in increased starch degradation, osmotic adjustment, antioxidants activity, and dehydrins accumulation during seed germination under water deficient condition.

Adaptability to High Temperature and Stay-Green Genotypes Associated With Variations in Antioxidant, Chlorophyll Metabolism, and γ-Aminobutyric Acid Accumulation in Creeping Bentgrass Species

High temperature limits the cultivation and utilization of cool-season plants in many regions worldwide. Recently, extreme hot waves swept across the globe in summer, leading to enormous economic loss. The evaluation and identification of genotypic variation in thermotolerance within species are critical to breeding for environmental adaptation and also provide potential materials to explore thermo-resistant mechanism in plants. Forty-two accessions of creeping bentgrass (Agrostis stolonifera), which is a cool-season perennial grass for turf and ecological remediation, were collected from 15 different countries. Physiological traits, namely, chlorophyll (Chl) content, electrolyte leakage, photochemical efficiency, performance index on absorption basis, leaf relative water content, and osmotic potential were used to evaluate the heat tolerance of these materials in controlled growth chambers and field during summer. Stay-green and early-aging genotypes were selected to further reveal the potential mechanism of tolerance to senescence and heat damage associated with alterations in Chl metabolism, antioxidant and photosynthetic capacity, and endogenous γ-aminobutyric acid (GABA). Findings showed that there were significant genetic variations in physiological traits among 41 materials in response to high temperature stress. The 13M, PROVIDENCE, and LOFTS L-93 were the top three accessions with superior tolerance to heat and summer stress than other materials in terms of laboratory and field tests. In response to heat stress, the stay-green genotype PROVIDENCE exhibited significantly higher photochemical efficiency, net photosynthetic rate, transpiration rate, and water use efficiency than the heat-susceptible W6 6570. Delayed leaf senescence in relation to less Chl loss was detected in the PROVIDENCE associated with maintenance of significantly higher expression levels of Chl-anabolic genes (AsCHLH, AsPBGD, and AsPOR) and lower Chl-catabolic gene AsPPH under heat stress. Genetic attributes, such as better capacity to scavenge reactive oxygen species and higher endogenous GABA content could play positive roles in alleviating heat-induced senescence, oxidative damage, and metabolic disturbance in the PROVIDENCE.

Chitosan regulates metabolic balance, polyamine accumulation, and Na+ transport contributing to salt tolerance in creeping bentgrass

BACKGROUND

Chitosan (CTS), a natural polysaccharide, exhibits multiple functions of stress adaptation regulation in plants. However, effects and mechanism of CTS on alleviating salt stress damage are still not fully understood. Objectives of this study were to investigate the function of CTS on improving salt tolerance associated with metabolic balance, polyamine (PAs) accumulation, and Na+ transport in creeping bentgrass (Agrostis stolonifera).

RESULTS

CTS pretreatment significantly alleviated declines in relative water content, photosynthesis, photochemical efficiency, and water use efficiency in leaves under salt stress. Exogenous CTS increased endogenous PAs accumulation, antioxidant enzyme (SOD, POD, and CAT) activities, and sucrose accumulation and metabolism through the activation of sucrose synthase and pyruvate kinase activities, and inhibition of invertase activity. The CTS also improved total amino acids, glutamic acid, and γ-aminobutyric acid (GABA) accumulation. In addition, CTS-pretreated plants exhibited significantly higher Na+ content in roots and lower Na+ accumulation in leaves then untreated plants in response to salt stress. However, CTS had no significant effects on K+/Na+ ratio. Importantly, CTS enhanced salt overly sensitive (SOS) pathways and also up-regulated the expression of AsHKT1 and genes (AsNHX4, AsNHX5, and AsNHX6) encoding Na+/H+ exchangers under salt stress.

CONCLUSIONS

The application of CTS increased antioxidant enzyme activities, thereby reducing oxidative damage to roots and leaves. CTS-induced increases in sucrose and GABA accumulation and metabolism played important roles in osmotic adjustment and energy metabolism during salt stress. The CTS also enhanced SOS pathway associated with Na+ excretion from cytosol into rhizosphere, increased AsHKT1 expression inhibiting Na+ transport to the photosynthetic tissues, and also up-regulated the expression of AsNHX4, AsNHX5, and AsNHX6 promoting the capacity of Na+ compartmentalization in roots and leaves under salt stress. In addition, CTS-induced PAs accumulation could be an important regulatory mechanism contributing to enhanced salt tolerance. These findings reveal new functions of CTS on regulating Na+ transport, enhancing sugars and amino acids metabolism for osmotic adjustment and energy supply, and increasing PAs accumulation when creeping bentgrass responds to salt stress.

Amelioration of salt induced toxicity in pearl millet by seed priming with silver nanoparticles (AgNPs): The oxidative damage, antioxidant enzymes and ions uptake are major determinants of salt tolerant capacity

Abiotic stresses in plants reduce crop growth and productivity. Nanoparticles (NPs) are effectively involved in the physiochemical processes of crop plants, especially under the abiotic stresses; whereas, less information is available regarding the role of AgNPs in salt-stressed plants. Therefore, in the current study, we investigated the effects of seed priming with commercially available silver nanoparticles (AgNPs) (size range between 50 and 100 nm) on plant morphology, physiology, and antioxidant defence system of pearl millet (Pennisetum glaucum L.) under different concentrations of salt stress (0, 120 and 150 mM NaCl). The seed priming with AgNPs at different levels (0, 10, 20 and 30 mM) mitigated the adverse impacts of salt stress and improved plant growth and defence system. The results demonstrated that salt-stressed plants had restricted growth and a noticeable decline in fresh and dry weight. Salt stress enhanced the oxidative damage by excessive production of hydrogen peroxide (H₂O₂), malondialdehyde (MDA) contents in pearl millet leaves. However, seed priming with AgNPs significantly improved the plant height growth related attributes, relative water content, proline contents and ultimately fresh and dry weight at 20 mM AgNPs alone or with salt stress. The AgNPs reduced the oxidative damage by improving antioxidant enzyme activities in the pearl millet leaves under salt stress. Furthermore, sodium (Na⁺) and Na⁺/K⁺ ratio was decreased and potassium (K⁺) increased by NPs, and the interactive effects between salt and AgNPs significantly impacted the total phenolic and flavonoid content in pearl millet. It was concluded that seed priming with AgNPs could enhance salinity tolerance in crop plants by enhancing physiological and biochemical responses. This might boost global crop production in salt-degraded lands.

Spermine Regulates Water Balance Associated with Ca2+-Dependent Aquaporin (TrTIP2-1, TrTIP2-2 and TrPIP2-7) Expression in Plants under Water Stress

Spermine (Spm) regulates water balance involved in water channel proteins, aquaporins (AQPs), in plants. An increase in endogenous Spm content via exogenous Spm application significantly improved cell membrane stability, photosynthesis, osmotic adjustment (OA) and water use efficiency (WUE) contributing to enhanced tolerance to water stress in white clover. Spm upregulated TrTIP2-1, TrTIP2-2 and TrPIP2-7 expressions and also increased the abundance of TIP2 and PIP2-7 proteins in white clover under water stress. Spm quickly activated intracellular Ca2+ signaling and Spm-induced TrTIP2-2 and TrPIP2-7 expressions could be blocked by Ca2+ channel blockers and the inhibitor of Ca2+-dependent protein kinase in leaves of white clover. TrSAMS in relation to Spm biosynthesis was first cloned from white clover and the TrSAMS was located in the nucleus. Transgenic Arabidopsis overexpressing the TrSAMS had significantly higher endogenous Spm content and improved cell membrane stability, photosynthesis, OA, WUE and transcript levels of AtSIP1-1, AtSIP1-2, AtTIP2-1, AtTIP2-2, AtPIP1-2, AtPIP2-1 and AtNIP2-1 than wild type in response to water stress. Current findings indicate that Spm regulates water balance via an enhancement in OA, WUE and water transport related to Ca2+-dependent AQP expression in plants under water stress.

Indole-3-acetic acid improves drought tolerance of white clover via activating auxin, abscisic acid and jasmonic acid related genes and inhibiting senescence genes

BACKGROUND

Auxin may have a positive effect on plants under drought stress. White clover is widely cultivated and often prone to water shortages. In the present study, we investigated the effects of exogenous indole - 3-acetic acid (IAA) on growth and physiological changes of white clover under drought stress condition. The contents of endogenous IAA and other hormones including ABA, CTK, JA, GA, IAA, and SA were assayed. Moreover, expressions of auxin-responsive genes, drought-responsive genes and leaf senescence-associated genes were detected in response to exogenous IAA.

RESULTS

Compared to control, drought stress alone significantly diminished stem dry weigh, relative water content (RWC) and total chlorophyll content (Chl). Exogenous IAA treatment significantly increased RWC and Chl, whereas L-AOPP treatment drastically decreased stem dry weight, RWC and Chl under drought stress condition. Additionally, exogenous IAA treatment significantly increased ABA content and JA content, up-regulated expression of auxin responsive genes (GH3.1, GH3.9, IAA8), drought stress responsive genes (bZIP11, DREB2, MYB14, MYB48, WRKY2, WRKY56, WRKY108715 and RD22), and down-regulated expressions of auxin-responding genes (GH3.3, GH3.6, IAA27) and leaf senescence genes (SAG101 and SAG102) in the presence of PEG. Contrarily, L-AOPP treatment significantly reduced contents of ABA, GA3 and JA, down-regulated expressions of GH3.1, GH3.9, IAA8, bZIP11, DREB2, MYB14, MYB48, WRKY2, WRKY56, WRKY108715, ERD and RD22, and up-regulated SAG101 and SAG102.

CONCLUSIONS

Exogenous IAA improved drought tolerance of white clover possibly due to endogenous plant hormone concentration changes and modulation of genes involving in drought stress response and leaf senescence. These results provided useful information to understand mechanisms of IAA improved drought tolerance in white clover.

Selenium and Salt Interactions in Black Gram (Vigna mungo L): Ion Uptake, Antioxidant Defense System, and Photochemistry Efficiency

Salinity is a major abiotic stress which limits crop production, especially under rainfed conditions. Selenium (Se), as an important micronutrient, plays a vital role in mitigating detrimental effects of different abiotic stresses. The objective of this research was to examine the effect of Se fertilization on black gram (Vigna mungo) under salt stress. Our results showed that salt stress (100 mM NaCl) in leaves significantly induced oxidative damage and caused a decline in relative water content, chlorophyll (Chl), stomatal conductance (gs), photochemical efficiency (Fv/Fm), sucrose, and reducing sugars. A low dose of Se (1.5 ppm) significantly reduced hydrogen peroxide content, malondialdehyde formation, cell membrane damage, and also improved antioxidative enzyme activities, including superoxide dismutase, catalase, ascorbate peroxidase, glutathione reductase, and glutathione peroxidase under salt stress. Se-treated plants exhibited higher Chl, gs, Fv/Fm, sucrose, and reducing sugars than untreated plants in response to salt stress. In addition, Se application enhanced Se uptake and reduced Na+ uptake, but Cl- remained unaffected. Our results indicated that a low dose of Se effectively alleviated salt damage via inhibition of Na+ uptake and enhanced antioxidant defense resulting in a significant decrease in oxidative damage, and maintained gaseous exchange and PS II function for sucrose and reducing sugars accumulation in black gram.

BBS5 and INPP5E mutations associated with ciliopathy disorders in families from Pakistan

Ciliopathies are a clinically and genetically heterogeneous group of disorders often exhibiting phenotypic overlap and caused by abnormalities in the structure or function of cellular cilia. As such, a precise molecular diagnosis is important for guiding clinical management and genetic counseling. In the present study, two Pakistani families comprising individuals with overlapping clinical features suggestive of a ciliopathy syndrome, including intellectual disability, obesity, congenital retinal dystrophy, and hypogonadism (in males), were investigated clinically and genetically. Whole-exome sequencing identified the likely causes of disease as a novel homozygous frameshift mutation (NM_152384.2: c.196delA; p.(Arg66Glufs*12); family 1) in BBS5, and a nonsense mutation (NM_019892.5:c.1879C>T; p.Gln627*; family 2) in INPP5E, previously reported in an extended Pakistani family with MORM syndrome. Our findings expand the molecular spectrum associated with BBS5 mutations in Pakistan and provide further supportive evidence that the INPP5E mutation is a common cause of ciliopathy in Northern Pakistan, likely representing a regional founder mutation. This study also highlights the value of genomic studies in Pakistan for families affected by rare heterogeneous developmental disorders and where clinical phenotyping may be limited by geographical and financial constraints. The identification of the spectrum and frequency of disease-causing variants within this setting enables the development of population-specific genetic testing strategies targeting variants common to the local population and improving health care outcomes.

Effect of planting patterns on yield, nutrient accumulation and distribution in maize and soybean under relay intercropping systems

Planting patterns affect nitrogen (N), phosphorus (P), and potassium (K) acquisition and distribution in maize and soybean under intercropping conditions. Here we reveal that strip relay-intercropping increases the N, P, and K uptake and distribution across plant organs (root, straw, and seed) of maize and soybean, accelerates the dry-matter production of intercrop-species, and compensates the slight maize yield loss by considerably increasing the soybean yield. In a two-year experiment, soybean was planted with maize in different planting patterns (SI, 50:50 cm and SII, 40:160 cm) of relay-intercropping, both planting patterns were compared with sole cropping of maize (SM) and soybean (SS). As compared to SI, SII increased the N, P, and K accumulation in each organ of soybean by 20, 32, and 18 (root) %, 71, 61, and 76 (straw) %, and 68, 65, and 62 (seed) %, respectively, whereas decreased the N, P, and K accumulation in each organ of maize by 1, 4, and 8 (root) %, 1, 10, and 3 (straw) %, and 5, 10, and 8 (seed) %, respectively. Overall, in SII, relay-cropped soybean accumulated 91% of total nutrient uptake (TNU) of sole soybean plants, and relay-cropped maize accumulated 94% of TNU of sole maize plants.

Novel candidate genes and variants underlying autosomal recessive neurodevelopmental disorders with intellectual disability

Identification of Mendelian genes for neurodevelopmental disorders using exome sequencing to study autosomal recessive (AR) consanguineous pedigrees has been highly successful. To identify causal variants for syndromic and non-syndromic intellectual disability (ID), exome sequencing was performed using DNA samples from 22 consanguineous Pakistani families with ARID, of which 21 have additional phenotypes including microcephaly. To aid in variant identification, homozygosity mapping and linkage analysis were performed. DNA samples from affected family member(s) from every pedigree underwent exome sequencing. Identified rare damaging exome variants were tested for co-segregation with ID using Sanger sequencing. For seven ARID families, variants were identified in genes not previously associated with ID, including: EI24, FXR1 and TET3 for which knockout mouse models have brain defects; and CACNG7 and TRAPPC10 where cell studies suggest roles in important neural pathways. For two families, the novel ARID genes CARNMT1 and GARNL3 lie within previously reported ID microdeletion regions. We also observed homozygous variants in two ID candidate genes, GRAMD1B and TBRG1, for which each has been previously reported in a single family. An additional 14 families have homozygous variants in established ID genes, of which 11 variants are novel. All ARID genes have increased expression in specific structures of the developing and adult human brain and 91% of the genes are differentially expressed in utero or during early childhood. The identification of novel ARID candidate genes and variants adds to the knowledge base that is required to further understand human brain function and development.

An analysis of NESTROFT and Red cell indices in evaluating antenatal mothers for Beta Thalassemia trait

Background: The frequency of thalassemia trait is about 3% worldwide, while in developing countries like India, it is a major cause of burden on the health care system. Naked eye single tube red cell osmotic fragility test (NESTROFT) used in population screening for beta thalassemia trait. It is a simple, low cost, reliable and most suitable screening test for β BTT, with a sensitivity of 99.8% in regions with high prevalence rates.Material &Methods: The present study was conducted in the Department of Pathology and included a total of 174 antenatal cases, attending the Out Patient Department of Obstetrics and Gynecology of a tertiary health care center in New Delhi between June 2011 to January 2012. The aim of the study was to screen mothers antenatally for early detection of BTT and to test the validity of NESTROFT in detection of thalassemic carriers of this area.Results: 174 pregnant women attending antenatal clinics were screened for detecting hemoglobinopathy with the help of NESTROFT, red cell indices, haemoglobin electrophoresis and HPLC It was seen that only four cases were BTT while ten were of microcytic anaemia and two had normal red cell indices.Conclusion: antenatal diagnosis of BTT is an important screening programme to reduce the burden of birth of children suffering from thalassemia and other hemoglobinopathies.Bangladesh Journal of Medical Science Vol.17(3) 2018 p.411-416

Chorea-acanthocytosis: Homozygous 1-kb deletion in VPS13A detected by whole-genome sequencing

Objective

To determine a molecular diagnosis for a large multigenerational family of South Asian ancestry with seizures, hyperactivity, and episodes of tongue biting.

Methods

Two affected individuals from the family were analyzed by whole-genome sequencing on the Illumina HiSeq X platform, and rare variants were prioritized for interpretation with respect to the phenotype.

Results

A previously undescribed, 1-kb homozygous deletion was identified in both individuals sequenced, which spanned 2 exons of the VPS13A gene, and was found to segregate in other family members.

Conclusions

VPS13A is associated with autosomal recessive chorea-acanthocytosis, a diagnosis consistent with the phenotype observed in this family. Whole-genome sequencing presents a comprehensive and agnostic approach for detecting diagnostic mutations in families with rare neurologic disorders.

Identification of novel L2HGDH mutation in a large consanguineous Pakistani family- a case report

Background

L-2-hydroxyglutaric aciduria (L2HGA) is a progressive neurometabolic disease of brain caused by mutations of in L-2-hydroxyglutarate dehydrogenase (L2HGDH) gene. Cardinal clinical features include cerebellar ataxia, epilepsy, neurodevelopmental delay, intellectual disability, and other clinical neurological deficits.

Case presentation

We describe an index case of the family presented with generalised tonic-clonic seizure, developmental delay, intellectual disability, and ataxia. Initially, the differential diagnosis was difficult to be established and a SNP genome wide scan identified the candidate region on chromosome 14q22.1. DNA sequencing showed a novel homozygous mutation in the candidate gene L2HGDH (NM_024884.2: c.178G > A; p.Gly60Arg). The mutation p.Gly60Arg lies in the highly conserved FAD/NAD(P)-binding domain of this mitochondrial enzyme, predicted to disturb enzymatic function.

Conclusions

The combination of homozygosity mapping and DNA sequencing identified a novel mutation in Pakistani family with variable clinical features. This is second report of a mutation in L2HGDH gene from Pakistan and the largest family with L2HGA reported to date.

Three Mutations in the Bilateral Frontoparietal Polymicrogyria Gene GPR56 in Pakistani Intellectual Disability Families

Bilateral frontoparietal polymicrogyria (BFPP, MIM 606854) is a heterogeneous autosomal recessive disorder of abnormal cortical lamination, leading to moderate-to-severe intellectual disability (ID), seizure disorder, and motor difficulties, and caused by mutations in the G protein-coupled receptor 56 ( GPR56 ) gene. Twenty-eight mutations in 40 different families have been reported in the literature. The clinical and neuroimaging phenotype is consistent in these cases. The BFPP cortex consists of numerous small gyral cells, with scalloping of the cortical-white matter junction. There are also associated white matter, brain stem, and cerebellar changes. GPR56 is a member of an adhesion G protein-coupled receptor family with a very long N-terminal stalk and seven transmembrane domains. In this study, we identified three families from Pakistan, ascertained primarily for ID, with overlapping approximately 1 Mb region (chr16:56,973,335-57,942,866) of homozygosity by descent, including 24 RefSeq genes. We found three GPR56 homozygous mutations, using next-generation sequencing. These mutations include a substitutional variant, c.1460T > C; p.L487P, (chr16:57693480 T > C), a 13-bp insertion causing the frameshift and truncating mutation, p.Leu269Hisfs*21 (NM_005682.6:c.803_804insCCATGGAGGTGCT; Chr16: 57689345_57689346insCCATGGAGGTGCT), and a truncating mutation c.1426C > T; p.Arg476* (Chr16:57693446C > T). These mutations fully segregated with ID in these families and were absent in the Exome Aggregation Consortium database that has approximately 8,000 control samples of South Asian origin. Two of these mutations have been reported in ClinVar database, and the third one has not been reported before. Three families from Pakistan with GPR56 mutations have been reported before. With the addition of our findings, the total number of mutations reported in Pakistani patients now is six. These results increase our knowledge regarding the mutational spectrum of the GPR56 gene causing BFPP/ID.

Adnexal Tumors of Skin: An Experience at a Tertiary Care Center at Delhi

Background:

Adnexal skin tumors are a heterogeneous group of uncommon tumors usually misdiagnosed clinically due to a huge variety of types and their variants. Histopathology usually helps in establishing the diagnosis.

Aims:

The study was undertaken to analyze the morphological, clinical, and histological features of adnexal tumors (ATs) of the skin at our center over a period of 4 years.

Subjects and Methods:

retrospective study was conducted over a period of 4 years (April 2010–March 2014), comprising 25 ATs of skin diagnosed in the Department of Pathology, Hamdard Institute of Medical Sciences and Research, Jamia Hamdard, New Delhi. All the consecutively reported AT cases were reviewed and reclassified as AT arising from sebaceous glands, hair follicles, or sweat glands. The concordance of clinical and histopathological diagnosis was also assessed.

Results:

Most of the ATs were benign (24/25) with head and neck being the most common location (72%). Nearly 56% of the tumors exhibited sweat gland differentiation, 28% hair follicle differentiation, and sebaceous gland tumors accounted for 16%. The most common varieties of tumors encountered in the present study included hidradenoma papilliferum and pilomatricoma. The concordance between clinical and histopathological diagnosis was found to be 50% approximately.

Conclusions:

ATs of the skin are rare neoplasms with benign tumors being far more common. They are often misdiagnosed clinically, so histopathology remains the gold standard for establishing an accurate diagnosis of skin ATs.

Autosomal-Recessive Hearing Impairment Due to Rare Missense Variants within S1PR2

The sphingosine-1-phosphate receptors (S1PRs) are a well-studied class of transmembrane G protein-coupled sphingolipid receptors that mediate multiple cellular processes. However, S1PRs have not been previously reported to be involved in the genetic etiology of human traits. S1PR2 lies within the autosomal-recessive nonsyndromic hearing impairment (ARNSHI) locus DFNB68 on 19p13.2. From exome sequence data we identified two pathogenic S1PR2 variants, c.323G>C (p.Arg108Pro) and c.419A>G (p.Tyr140Cys). Each of these variants co-segregates with congenital profound hearing impairment in consanguineous Pakistani families with maximum LOD scores of 6.4 for family DEM4154 and 3.3 for family PKDF1400. Neither S1PR2 missense variant was reported among ∼120,000 chromosomes in the Exome Aggregation Consortium database, in 76 unrelated Pakistani exomes, or in 720 Pakistani control chromosomes. Both DNA variants affect highly conserved residues of S1PR2 and are predicted to be damaging by multiple bioinformatics tools. Molecular modeling predicts that these variants affect binding of sphingosine-1-phosphate (p.Arg108Pro) and G protein docking (p.Tyr140Cys). In the previously reported S1pr2(-/-) mice, stria vascularis abnormalities, organ of Corti degeneration, and profound hearing loss were observed. Additionally, hair cell defects were seen in both knockout mice and morphant zebrafish. Family PKDF1400 presents with ARNSHI, which is consistent with the lack of gross malformations in S1pr2(-/-) mice, whereas family DEM4154 has lower limb malformations in addition to hearing loss. Our findings suggest the possibility of developing therapies against hair cell damage (e.g., from ototoxic drugs) through targeted stimulation of S1PR2.

In silico analysis of SIGMAR1 variant (rs4879809) segregating in a consanguineous Pakistani family showing amyotrophic lateral sclerosis without frontotemporal lobar dementia

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder affecting upper motor neurons in the brain and lower motor neurons in the brain stem and spinal cord, resulting in fatal paralysis. It has been found to be associated with frontotemporal lobar degeneration (FTLD). In the present study, we have described homozygosity mapping and gene sequencing in a consanguineous autosomal recessive Pakistani family showing non-juvenile ALS without signs of FTLD. Gene mapping was carried out in all recruited family members using microsatellite markers, and linkage was established with sigma non-opioid intracellular receptor 1 (SIGMAR1) gene at chromosome 9p13.2. Gene sequencing of SIGMAR1 revealed a novel 3'-UTR nucleotide variation c.672*31A>G (rs4879809) segregating with disease in this family. The C9ORF72 repeat region in intron 1, previously implicated in a related phenotype, was excluded through linkage, and further confirmation of exclusion was obtained by amplifying intron 1 of C9ORF72 with multiple primers in affected individuals and controls. In silico analysis was carried out to explore the possible role of 3'-UTR variant of SIGMAR1 in ALS. The Regulatory RNA motif and Element Finder program revealed disturbance in miRNA (hsa-miR-1205) binding site due to this variation. ESEFinder analysis showed new SRSF1 and SRSF1-IgM-BRCA1 binding sites with significant scores due to this variation. Our results indicate that the 3'-UTR SIGMAR1 variant c.672*31A>G may have a role in the pathogenesis of ALS in this family.

Association between tumour necrosis-α gene polymorphisms and acne vulgaris in a Pakistani population

BACKGROUND

The cytokine tumour necrosis factor (TNF)-α is a well-studied potent candidate mediator that is systemically involved in a variety of inflammatory diseases. Several single nucleotide polymorphisms (SNPs) of the TNF-α gene have been studied with regard the pathogenesis of acne vulgaris, but the results have been inconclusive.

AIM

This case-control study investigated the association of the TNF -308 G>A and -238 G>A SNPs with acne vulgaris in a high-risk Pakistani population.

METHODS

In total, 160 healthy controls and 140 patients with acne were enrolled in this study. Polymorphisms were determined by PCR and restriction fragment length polymorphism analysis.

RESULTS

Our data showed that the TNF -308 G>A and TNF -238 G>A SNPs were present at a significantly higher rate in cases than in controls (P < 0.01 and P < 0.02; respectively). There was a significant difference between the G and A alleles from patients with acne and controls for -308 G>A (OR = 1.5, 95% CI = 1.07-2.19, P < 0.02) and -238 G>A (OR=1.6, 95% CI = 1.06-2.44, P = 0.02) genotype. Moreover, the severity of acne was significantly associated with TNF genotype (TNF -308 G>A: χ² = 34.6, P < 0.001; TNF -238 G>AL χ² = 12.9, P < 0.01).

CONCLUSION

Our data suggest that the TNF -308 G>A and TNF -238 G>A SNPs may contribute to the pathogenesis of acne in the study population. Furthermore, patients with severe acne showed an increased frequency of mutant TNF genotypes at -308 and -238 compared with patients with less severe acne.

Bone marrow negative visceral leishmaniasis in an adolescent male

Visceral Leishmaniasis or Kala Azar is endemic in certain regions of India. In endemic areas, the constellation of fever, progressive weight loss, weakness, pronounced splenomegaly, anemia, leukopenia, and hypergammaglobulinemia is highly suggestive of visceral leishmaniasis. Demonstration of the parasite in liver, splenic or bone marrow aspirates is confirmatory. We present a case in which Leishmania donovani (LD) bodies were demonstrated on splenic aspirate. We were unable to demonstrate LD bodies on bone marrow aspiration.

Mutations in WDR62 gene in Pakistani families with autosomal recessive primary microcephaly

Background

Autosomal recessive primary microcephaly is a disorder of neurogenic mitosis that causes reduction in brain size. It is a rare heterogeneous condition with seven causative genes reported to date. Mutations in WD repeat protein 62 are associated with autosomal recessive primary microcephaly with cortical malformations. This study was initiated to screen WDR62 mutations in four consanguineous Pakistani families with autosomal recessive primary microcephaly.

Methods

As part of a large study to detect the genetic basis of primary microcephaly in Pakistan, homozygosity mapping and DNA sequencing was used to explore the genetic basis of autosomal recessive primary microcephaly in four families.

Results

Four out of 100 families recruited in the study revealed linkage to the MCPH2 locus on chromosome 19, which harbor WDR62 gene. DNA sequencing in these MCPH2 linked families result in the identification of a novel nonsense mutation (p.Q648X) and three previously known mutations.

Conclusion

Our data indicate that WDR62 mutations cause about 4% of autosomal recessive primary microcephaly in Pakistan.

A novel splice site mutation in the EDAR gene underlies autosomal recessive hypohidrotic ectodermal dysplasia in a Pakistani family

Hypohidrotic ectodermal dysplasia is a rare congenital disorder that results in abnormalities in the structures of ectodermal origin: hair, teeth, and eccrine sweat glands. DNA sequence analysis of EDAR gene in a Pakistani family, demonstrating autosomal recessive form of hypohidrotic ectodermal dysplasia, identified a novel homozygous mutation affecting splice donor site of exon 5 [IVS5+1G > or = C] of the gene.

Leiomyoma of scrotum

Leiomyoma is a benign tumor of smooth muscles. Leiomyoma originating from the scrotum is a rare entity. We report here a case of 50-year-old male who presented with a 4-cm lump in the left side of scrotum. Clinically, it was provisionally diagnosed as sebaceous cyst and was excised. The histopathology showed findings consistent with leiomyoma. There was no cytological atypia or mitosis. The final diagnosis of solitary leiomyoma of scrotum was given. The patient was followed up regularly and is doing fine for last 4 months.

Novel protein-truncating mutations in the ASPM gene in families with autosomal recessive primary microcephaly

Autosomal recessive primary microcephaly (MCPH) is a neurodevelopmental disorder that causes reduction in brain size. Individuals affected with the disorder show a small but architecturally normal cerebral cortex and are associated with mental retardation of mild-to severe form. MCPH is genetically heterogeneous with six loci, and four genes have been identified so far. Homozygous mutations in the ASPM gene, located at MCPH5 locus on chromosome 1q31, are the most common cause of MCPH particularly in the Pakistani population. In the present study, we have ascertained ten Pakistani and one Kashmiri family with primary microcephaly. We screened for potential mutations of the ASPM gene in seven consanguineous families (six Pakistani and one Kashmiri) linked to MCPH5 locus. Two previously reported (8508delGA, W1326X) and four novel sequence variants (Y1712X, I1717X, Y3353X, R3244X) were detected and all were predicted to be protein truncating. The degree of mental retardation in the affected individuals of the seven families varied from mild to moderate, and was not dependent on the location of mutations in the ASPM gene.

A syndromic form of autosomal recessive congenital microcephaly (Jawad syndrome) maps to chromosome 18p11.22-q11.2

We report a consanguineous Pakistani family with seven affected individuals showing a syndromic form of congenital microcephaly. Clinical features of affected individuals include congenital microcephaly with sharply slopping forehead, moderate to severe mental retardation, anonychia congenita, and digital malformations. By screening human genome with microsatellite markers, this autosomal recessive condition was mapped to a 25.2 cM interval between markers D18S1150 and D18S1100 on chromosome 18p11.22-q12.3. However, the region of continuous homozygosity between markers D18S1150 and D18S997 spanning 15.33 cM, probably define the most likely candidate region for this condition. This region encompasses a physical distance of 12.03 Mb. The highest two-point LOD score of 3.03 was obtained with a marker D18S1104 and multipoint score reached a maximum of 3.43 with several markers. Six candidate genes, CEP76, ESCO1, SEH1L, TUBB6, ZNF519, and PTPN2 were sequenced, and were found to be negative for functional sequence variants.

Previously described sequence variant in CDK5RAP2 gene in a Pakistani family with autosomal recessive primary microcephaly

Background

Autosomal Recessive Primary Microcephaly (MCPH) is a disorder of neurogenic mitosis. MCPH leads to reduced cerebral cortical volume and hence, reduced head circumference associated with mental retardation of variable degree. Genetic heterogeneity is well documented in patients with MCPH with six loci known, while pathogenic sequence variants in four respective genes have been identified so far. Mutations in CDK5RAP2 gene at MCPH3 locus have been least involved in causing MCPH phenotype.

Methods

All coding exons and exon/intron splice junctions of CDK5RAP2 gene were sequenced in affected and normal individuals of Pakistani MCPH family of Kashmiri origin, which showed linkage to MCPH3 locus on chromosome 9q33.2.

Results

A previously described nonsense mutation [243 T>A (S81X)] in exon 4 of CDK5RAP2 gene has been identified in the Pakistani family, presented here, with MCPH Phenotype. Genomic and cDNA sequence comparison revealed that the exact nomenclature for this mutation is 246 T>A (Y82X).

Conclusion

Recurrent observation of Y82X mutation in CDK5RAP2 gene in this Pakistani family may be a sign of confinement of a rare ancestral haplotype carrying this pathogenic variant within Northern Pakistani population, as this has not been reported in any other population.

Ectodermal dysplasia of hair and nail type: mapping of a novel locus to chromosome 17p12-q21.2

BACKGROUND

Ectodermal dysplasias (EDs) describe a large and complex group of disorders characterized by abnormal development of the skin and appendages (hair, nails, teeth and sweat glands). Of the approximately 200 different EDs, about 30 have been studied at the molecular level. In an effort to understand the molecular bases of ED of hair and nail type, we studied a Pakistani consanguineous family with multiple affected individuals.

OBJECTIVES

To localize the gene responsible for the autosomal recessive form of ED of hair and nail type.

METHODS

Genotyping of nine members of the family, including five affected and four normal individuals was performed using microsatellite markers mapping to candidate regions, harbouring genes involved in related phenotypes. Five epithelial keratin genes located in the candidate region were sequenced to identify the pathogenic mutation.

RESULTS

We mapped the disease locus to a 24.2-cM interval flanked by markers D17S839 and D17S1299 on chromosome 17p12-q21.2 (Z(max) = 4.4). DNA sequencing of five epithelial keratin candidate genes, present in the disease locus, did not reveal any pathogenic mutation in the affected individuals.

CONCLUSIONS

The gene for ED of hair and nail type has been mapped to chromosome 17p12-q21.2 in a Pakistani consanguineous family. Failure to detect mutations in epithelial keratin genes suggests that the mutation may lie either in regulatory regions of one of the epithelial keratin genes or in another unknown gene, located in the linkage interval, with a possible role in the development of ectodermal appendages.

A novel locus for alopecia with mental retardation syndrome (APMR2) maps to chromosome 3q26.2-q26.31

Congenital alopecia may occur either alone or in association with ectodermal and other abnormalities. On the bases of such associations, several different syndromes featuring congenital alopecia can be distinguished. Alopecia with mental retardation syndrome (APMR) is a rare autosomal recessive disorder, clinically characterized by total or partial hair loss and mental retardation. In the present study, a five-generation Pakistani family with multiple affected individuals with APMR was ascertained. Patients in this family exhibited typical features of APMR syndrome. The disease locus was mapped to chromosome 3q26.2-q26.31 by carrying out a genome scan followed by fine mapping. A maximum two-point logarithm of odds (LOD) score of 2.93 at theta=0.0 was obtained at markers D3S3053 and D3S2309. Multipoint linkage analysis resulted in a maximum LOD score of 4.57 with several markers, which supports the linkage. The disease locus was flanked by markers D3S1564 and D3S2427, which corresponds to 9.6-cM region according to the Rutgers combined linkage-physical map of the human genome (build 35) and contains 5.6 Mb. The linkage interval of the APMR locus identified here does not overlap with the one described previously; therefore, this locus has been designated as APMR2.